Abstract: In this review, we present many different classes of ecological relationships in which are registered interactions among algal and bacterial organisms. The uses of molecular techniques as metagenomics to test hypothesis, evaluate subjacent processes and searching for patterns in microbial communities are included and discussed. Our documental research suggests that great advances have been accomplished in this discipline until now, and many of these advances were through metagenomics application. Nevertheless, some questions and aspects of relations algae-bacteria remain not answered yet and metagenomics could be a power and useful working tool.